README

This is the README file for p4est.
p4est is a C library to manage a collection (a forest) of multiple
connected adaptive quadtrees or octrees in parallel.
Copyright (C) 2010 The University of Texas System
Additional copyright (C) 2011 individual authors
p4est is written by Carsten Burstedde, Lucas C. Wilcox, and Tobin Isaac
and released under the GNU General Public Licence version 2 (or later).
The official web page for source code and documentation is www.p4est.org.
Please send bug reports and ideas for contribution to info@p4est.org.
0. Acknowledgement and Disclaimer
The development of p4est was partially supported by the US National Science
Foundation (NSF Grants No. CCF-0427985, CMMI-1028889, CNS-0540372, CNS-0619838,
DMS-0724746, OCI-0749334, OPP-0941678) and the US Department of Energy (DOE
Grants No. 06ER25782, 08ER25860, SC0002710).
The authors thank the Texas Advanced
Computing Center (TACC) for providing them with access to the Ranger
supercomputer under NSF TeraGrid award MCA04N026, and the National Center for
Computational Science (NCCS) for early-user access to the Jaguar Cray XT5
supercomputer. Any opinions, findings and conclusions or recomendations
expressed in the source code and documentation are those of the authors and do
not necessarily reflect the views of the National Science Foundation (NSF).
1. Purpose
Many applications in applied mathematics and numerical simulation use a mesh of
computational cells that covers the domain of interest. The numerical solution
is then approximated by functions, each of which is associated with a small set
of cells (or even one). Dynamic ``adaptive'' methods change the mesh during
the simulation by local refinement or coarsening, and ``parallel'' methods
distribute (``partition'') the mesh between multiple processors, where each
processor ideally receives an equal share of the computational load. p4est
isolates the task of parallel dynamic adaptive mesh refinement (AMR),
coarsening, and load balancing, and encapsulates algorithms that scale well to
large numbers (10^5) of processors.
These algorithms are predominantly used for the numerical solution of partial
differential equations, but also support various other tasks where fast
hierarchical space subdivision is required, for example to locate particles in
space or to organize, sort, and search in large data sets.
2. Geometric structure
The basic structure used in p4est is a ``connectivity'' of quadtrees (2D) or
octrees (3D) that covers the domain of interest in a conforming macro-mesh.
This includes the case of using exactly one tree for representing the
hypercube. The trees can be arbitrarily refined and coarsened, where the
storage of quadrants/octants is distributed in parallel. Thus, the mesh
primitives used in p4est are quadrilaterals in 2D and hexahedra in 3D. The
adaptive structure allows for quadrants/octants of different sizes to neighbor
each other, which is commonly called ``non-conforming''. This concept leads to
``hanging'' faces and edges.
3. Core p4est (2D) and p8est (3D) routines
p?est_new: Create an equi-partitioned, uniformly refined forest.
p?est_refine: Adaptively subdivide octants based on a callback function, once
for each octant or recursively.
p?est_coarsen: Replace families of eight child octants by their common parent
octant, once or recursively.
p?est_partition: Redistribute the octants in parallel, according to a given
target number of octants for each process, or weights prescribed for all
octants.
p?est_balance: Ensure at most 2:1 size relations between neighboring octants by
local refinement where necessary.
p?est_checksum: Compute a partition-independent integer ``fingerprint'' of a
forest. This is useful for debugging and regression testing.
4. Interfacing to p4est from applications
p?est_ghost: Collect one layer of off-process octants touching the process
boundaries from the outside. This function requires a previous call to
p?est_balance. This is the most generally useful function for external
applications. By querying the ghost layer, the application can associate
degrees of freedom with the mesh which are the basis for all numerical
computation.
p?est_lnodes: Create a globally unique numbering of finite element degrees of
freedom for arbitrary order C0 nodal polynomials, also known as GLL basis. The
function takes into account the classification into ``independent'' and
``hanging'' degrees of freedom. Numberings for standard piecewise d-linear
finite elements or lowest-order Raviart-Thomas velocity variables are created
by calling this function with the parameters degree = 1 and -1, respectively.
This function requires previous calls to p?est_balance and p?est_ghost.
p?est_nodes: Like p?est_lnodes, but only for piecewise linear finite elements.
Technically no longer required, but we keep it around for its simplicity.
5. Installation from a release tarball
IMPORTANT NOTE:
Our official tarballs are linked from http://www.p4est.org/ and work fine.
The tarballs under
https://github.com/cburstedde/p4est/releases/
are created by github and are NOT endorsed by us. In particular, they are
missing the subdirectory sc, the configure script, and other generated files.
p4est uses the GNU autoconf/automake/libtool build system. See the INSTALL
file for details. Our official tarballs contain the configure script and all
required files. The following configure options are commonly used.
--enable-mpi is necessary for parallel functionality. Without this option,
p4est does not require MPI, which is replaced by a dummy implementation that
always assumes an MPI_Comm_size of 1 and an MPI_Comm_rank of 0.
--enable-debug enables assertions and additional code for verification. This
is generally helpful for development, even if it is somewhat slower and
produces a lot of diagnostic log messages.
CFLAGS="-Wall -g -O0" is an example of setting flags for a development build
compiled with the GNU compilers. p4est is written in plain C and does not
require FFLAGS or CXXFLAGS.
So, with a gcc style compiler a good debug configure line would be
/path/to/configure CFLAGS="-O0 -g -Wall -Wuninitialized" \
--enable-debug --enable-mpi --disable-shared
and for a production build use for example
/path/to/configure CFLAGS="-O2 -Wall -Wno-unused-but-set-variable" \
--enable-mpi
Both in-source and out-of-source builds are supported. For a one-time
installation, ./configure can be called in the root directory of the unpacked
tree. For development or for testing multiple configure options, create an
empty directory for each configuration and invoke configure with a relative
path.
The subpackage 'sc' is contained in the tarball and used by default. It is
possible to use a version of sc that has been make install'd independently:
(1.) Create an empty directory and call sc/configure with its relative path.
Use --prefix=path-to-install-sc to specify the destination for the
compiled files. Then call make install.
(2.) Create another empty directory and call the p4est configure with its
relative path and the options --prefix=path-to-install-p4est and
--with-sc=path-to-install-sc. Make sure to use the same compiler flags
and configure options as in (1.). Finally, call make install.
This is the proposed procedure to split the p4est installation into two
packages, say for a linux binary distribution. The benefit is that other
packages that might require sc do not force p4est to get installed.
6. Installation from source
When installing from source, GNU autotools must be invoked to generate the
necessary configuration files and the configure script. A bootstrap script is
provided for this purpose: give the shell command './bootstrap' before
following the instructions in the INSTALL file. Then proceed as in 5.
7. Installation from git repository
If you have obtained p4est from a git repository, such as via the shell command
git clone https://github.com/cburstedde/p4est.git
then the libsc submodule, which resides in the subdirectory sc, must be
downloaded before configuring and compiling. This can be accomplished with the
shell commands
git submodule init; git submodule update
After the submodule has been obtained, install from source as described above
in 6.
8. Using p4est through the deal.II interface
The recent development version of the generic adaptive finite element software
library deal.II interfaces to p4est to parallelize its mesh handling. The most
convenient way to compile and install p4est to be accessible for deal.II is to
use the doc/p4est-setup.sh script. This creates both a debug and production
version compiled with minimal logging output. To know what is going on within
p4est, the log level needs to be relaxed in the script.
9. Building a release tarball from a git clone
The following script may be used to build a release tarball
#!/bin/sh
SRC_DIR=$(pwd)
WORK_DIR=$(mktemp -d)
cleanup() {
rm -rf "$WORK_DIR"
echo ""
echo "Deleted working directory $WORK_DIR"
}
trap cleanup EXIT
echo "Building p4est tarball in $WORK_DIR"
echo ""
# Get p4est
cd "$WORK_DIR"
git clone --recursive https://github.com/cburstedde/p4est
cd p4est
# Setup exclude files so that version number is not dirty
./bootstrap
./configure
git ls-files --others --exclude-standard >> .git/info/exclude
GIT_DIR=.git/modules/sc git ls-files --others --exclude-standard \
>> .git/modules/sc/info/exclude
echo ChangeLog >> .git/info/exclude
echo ChangeLog >> .git/modules/sc/info/exclude
git clean -xdf
git submodule foreach git clean -xdf
# Configure and build distribution tarball
./bootstrap
./configure
echo ""
echo "Building versions"
echo ""
git describe --dirty
git submodule foreach git describe --dirty
echo ""
make -j distcheck
mkdir -p "$SRC_DIR"
cp p4est-*.tar.gz "$SRC_DIR"